* Bug: ob-R.el breaks when :session is specified
@ 2022-05-15 6:00 Christian Heinrich
2022-05-15 8:08 ` Ihor Radchenko
0 siblings, 1 reply; 10+ messages in thread
From: Christian Heinrich @ 2022-05-15 6:00 UTC (permalink / raw)
To: emacs-orgmode; +Cc: Jeremie Juste
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Hi there,
I got back to an org file after upgrading to the latest release of org-mode and tried executing the
contained R source blocks. Unfortunately, emacs got stuck in the execution and was blocked; I had to
exit using C-g.
Here's a minimal example src block that causes emacs to get stuck:
#+begin_src R :results output :session *R* :exports both
a <- 10
a
#+end_src
R itself does start and the code is also executed correctly. However, the output from that session
is apparently not returned to emacs or the buffer.
When removing the :session argument it executes and returns as expected.
When bisecting this issue, I found that this commit causes it:
ac8c009e006197d2dad226dbe822d450aec23d23
lisp/ob-R.el: Fix session output with substrings matching prompts
Reverting it fixes the issue for earlier release (9.5.3) as well as for the current main branch.
The (with-current-buffer session ... ) somehow seems to break it for me, but I am unsure why no one
else here seems to experience this as the commit is from 2020?
Any suggestions?
Thanks!
Christian
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^ permalink raw reply [flat|nested] 10+ messages in thread
* Re: Bug: ob-R.el breaks when :session is specified
2022-05-15 6:00 Bug: ob-R.el breaks when :session is specified Christian Heinrich
@ 2022-05-15 8:08 ` Ihor Radchenko
2022-05-15 9:46 ` Christian Heinrich
2022-05-15 14:16 ` Jeremie Juste
0 siblings, 2 replies; 10+ messages in thread
From: Ihor Radchenko @ 2022-05-15 8:08 UTC (permalink / raw)
To: Christian Heinrich; +Cc: emacs-orgmode, Jeremie Juste
Christian Heinrich <com-orgmode-mailinglist@gladbachcity.de> writes:
> I got back to an org file after upgrading to the latest release of org-mode and tried executing the
> contained R source blocks. Unfortunately, emacs got stuck in the execution and was blocked; I had to
> exit using C-g.
>
> Here's a minimal example src block that causes emacs to get stuck:
>
> #+begin_src R :results output :session *R* :exports both
> a <- 10
> a
> #+end_src
>
> R itself does start and the code is also executed correctly. However, the output from that session
> is apparently not returned to emacs or the buffer.
I tried you example using Emacs >=26 and it works just fine.
Best,
Ihor
^ permalink raw reply [flat|nested] 10+ messages in thread
* Re: Bug: ob-R.el breaks when :session is specified
2022-05-15 8:08 ` Ihor Radchenko
@ 2022-05-15 9:46 ` Christian Heinrich
2022-05-15 19:58 ` Berry, Charles
2022-05-15 14:16 ` Jeremie Juste
1 sibling, 1 reply; 10+ messages in thread
From: Christian Heinrich @ 2022-05-15 9:46 UTC (permalink / raw)
To: Christian Heinrich; +Cc: emacs-orgmode
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Hi,
thanks, that's what I had expected since that patch has been around for a long time.
I run
emacs -q --load /tmp/init.el --file=/tmp/test.org
with my /tmp/init.el being only
> (require 'package)
> (package-initialize)
> (add-to-list 'load-path "~/.emacs.d/straight/repos/org/lisp/")
> (require 'org)
>
> ;(require 'ess-site)
> (org-babel-do-load-languages
> 'org-babel-load-languages
> '((R . t)))
I hope this constitutes a minimal example for a config - please correct me if I'm wrong.
My test.org contains the source block I had already posted:
#+begin_src R :results output :session *R* :exports both
a <- 10
a
#+end_src
Any ideas how I could continue to debug this? If I just remove that patch, everything works
flawlessly for me but I would like to figure out what causes the issues.
Thanks!
Christian
On Sun, 2022-05-15 at 16:08 +0800, Ihor Radchenko wrote:
> Christian Heinrich <com-orgmode-mailinglist@gladbachcity.de> writes:
>
> > I got back to an org file after upgrading to the latest release of org-mode and tried executing
> > the
> > contained R source blocks. Unfortunately, emacs got stuck in the execution and was blocked; I
> > had to
> > exit using C-g.
> >
> > Here's a minimal example src block that causes emacs to get stuck:
> >
> > #+begin_src R :results output :session *R* :exports both
> > a <- 10
> > a
> > #+end_src
> >
> > R itself does start and the code is also executed correctly. However, the output from that
> > session
> > is apparently not returned to emacs or the buffer.
>
> I tried you example using Emacs >=26 and it works just fine.
>
> Best,
> Ihor
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^ permalink raw reply [flat|nested] 10+ messages in thread
* Re: Bug: ob-R.el breaks when :session is specified
2022-05-15 8:08 ` Ihor Radchenko
2022-05-15 9:46 ` Christian Heinrich
@ 2022-05-15 14:16 ` Jeremie Juste
2022-05-15 18:06 ` Christian Heinrich
1 sibling, 1 reply; 10+ messages in thread
From: Jeremie Juste @ 2022-05-15 14:16 UTC (permalink / raw)
To: Ihor Radchenko; +Cc: Christian Heinrich, emacs-orgmode
Hello Christian,
Thanks for reporting but I cannot reproduce the bug with the org and
emacs version below.
Org mode version 9.5.3 (release_9.5.3-467-g2bd34e @
/home/djj/src/org-mode/lisp/)
GNU Emacs 27.2 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.24) of
2022-01-16
Can you please let me know which version of org-mode you are actually
using?
Ihor, many thanks for checking.
Best regards,
Jeremie
On Sunday, 15 May 2022 at 16:08, Ihor Radchenko wrote:
> Christian Heinrich <com-orgmode-mailinglist@gladbachcity.de> writes:
>
>> I got back to an org file after upgrading to the latest release of org-mode and tried executing the
>> contained R source blocks. Unfortunately, emacs got stuck in the execution and was blocked; I had to
>> exit using C-g.
>>
>> Here's a minimal example src block that causes emacs to get stuck:
>>
>> #+begin_src R :results output :session *R* :exports both
>> a <- 10
>> a
>> #+end_src
>>
>> R itself does start and the code is also executed correctly. However, the output from that session
>> is apparently not returned to emacs or the buffer.
>
> I tried you example using Emacs >=26 and it works just fine.
>
> Best,
> Ihor
^ permalink raw reply [flat|nested] 10+ messages in thread
* Re: Bug: ob-R.el breaks when :session is specified
2022-05-15 14:16 ` Jeremie Juste
@ 2022-05-15 18:06 ` Christian Heinrich
2022-05-15 22:21 ` Jeremie Juste
0 siblings, 1 reply; 10+ messages in thread
From: Christian Heinrich @ 2022-05-15 18:06 UTC (permalink / raw)
To: emacs-orgmode
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Hi Jeremie,
I just tested with
Org mode version 9.5.3 (release_9.5.3-504-gcdbb1c @
/home/heinrich/.emacs.d/straight/repos/org/lisp/)
using
GNU Emacs 27.1 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.30, cairo version 1.16.0) of 2021-
11-27, modified by Debian
I am on Debian Testing and that is the default emacs version.
Using the unmodified org (git hash from above) I get the following messages when executing a src
block with R:
executing R code block...
Loading ‘ess-bugs-l’: unescaped character literals `?(', `?)' detected, `?\(', `?\)' expected!
Type C-h m for help on ESS version 15.09
ess-tracebug mode enabled
Quit
Package cl is deprecated
Note that the "Quit" is me pressing Ctrl-g after a few seconds.
Removing the commit in question makes the block return instantaneously:
executing R code block...
Loading ‘ess-bugs-l’: unescaped character literals `?(', `?)' detected, `?\(', `?\)' expected!
Type C-h m for help on ESS version 15.09
ess-tracebug mode enabled
Code block evaluation complete.
Package cl is deprecated
I anticipated that this would not be obvious, since this feature is used too much to go unnoticed for
two years - but I am clueless as to how I should continue with debugging...
Thanks for your help!
Christian
On Sun, 2022-05-15 at 16:16 +0200, Jeremie Juste wrote:
>
> Hello Christian,
>
> Thanks for reporting but I cannot reproduce the bug with the org and
> emacs version below.
>
> Org mode version 9.5.3 (release_9.5.3-467-g2bd34e @
> /home/djj/src/org-mode/lisp/)
> GNU Emacs 27.2 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.24) of
> 2022-01-16
>
> Can you please let me know which version of org-mode you are actually
> using?
>
> Ihor, many thanks for checking.
>
> Best regards,
> Jeremie
>
> On Sunday, 15 May 2022 at 16:08, Ihor Radchenko wrote:
> > Christian Heinrich <com-orgmode-mailinglist@gladbachcity.de> writes:
> >
> > > I got back to an org file after upgrading to the latest release of org-mode and tried
> > > executing the
> > > contained R source blocks. Unfortunately, emacs got stuck in the execution and was blocked; I
> > > had to
> > > exit using C-g.
> > >
> > > Here's a minimal example src block that causes emacs to get stuck:
> > >
> > > #+begin_src R :results output :session *R* :exports both
> > > a <- 10
> > > a
> > > #+end_src
> > >
> > > R itself does start and the code is also executed correctly. However, the output from that
> > > session
> > > is apparently not returned to emacs or the buffer.
> >
> > I tried you example using Emacs >=26 and it works just fine.
> >
> > Best,
> > Ihor
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^ permalink raw reply [flat|nested] 10+ messages in thread
* Re: Bug: ob-R.el breaks when :session is specified
2022-05-15 9:46 ` Christian Heinrich
@ 2022-05-15 19:58 ` Berry, Charles
2022-05-16 5:26 ` Christian Heinrich
0 siblings, 1 reply; 10+ messages in thread
From: Berry, Charles @ 2022-05-15 19:58 UTC (permalink / raw)
To: Christian Heinrich; +Cc: emacs-orgmode
Um...
> On May 15, 2022, at 2:46 AM, Christian Heinrich <com-orgmode-mailinglist@gladbachcity.de> wrote:
>
> I run
>
> emacs -q --load /tmp/init.el --file=/tmp/test.org
>
> with my /tmp/init.el being only
>
>> (require 'package)
>> (package-initialize)
>> (add-to-list 'load-path "~/.emacs.d/straight/repos/org/lisp/")
>> (require 'org)
>>
>> ;(require 'ess-site)
The line above is commented out. So how do you load ess-site?
>> (org-babel-do-load-languages
>> 'org-babel-load-languages
>> '((R . t)))
>
> I hope this constitutes a minimal example for a config - please correct me if I'm wrong.
Just spitballing here:
Have you tried instrumenting `org-babel-R-evaluate-session'?
Maybe watching changes made to the session buffer on first evaluation and comparing to subsequent evals helps.
HTH,
Chuck
^ permalink raw reply [flat|nested] 10+ messages in thread
* Re: Bug: ob-R.el breaks when :session is specified
2022-05-15 18:06 ` Christian Heinrich
@ 2022-05-15 22:21 ` Jeremie Juste
2022-05-16 5:23 ` Christian Heinrich
2022-05-16 5:24 ` Christian Heinrich
0 siblings, 2 replies; 10+ messages in thread
From: Jeremie Juste @ 2022-05-15 22:21 UTC (permalink / raw)
To: Christian Heinrich; +Cc: emacs-orgmode
Hello Christian
On Sunday, 15 May 2022 at 20:06, Christian Heinrich wrote:
> I just tested with
>
> Org mode version 9.5.3 (release_9.5.3-504-gcdbb1c @
> /home/heinrich/.emacs.d/straight/repos/org/lisp/)
>
> using
>
> GNU Emacs 27.1 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.30, cairo version 1.16.0) of 2021-
> 11-27, modified by Debian
Many thanks for reporting back. I updated to gcdbb1c and it is still working fine.
My minimum working example is the following. From the org-mode root directory,
$ emacs -Q -L ./lisp -l org -l ~/ess-barebone.el
where ~/ess-barebone.el is the following:
#+begin_src elisp
(add-to-list 'load-path "/home/djj/.emacs.d/elpa/ess-20220125.2207/")
(require 'ess-r-mode)
(org-babel-do-load-languages
'org-babel-load-languages
'((R . t)))
(setq org-confirm-babel-evaluate nil)
#+end_src
Note that I'm still using a rather old ess version. Could you please try
with the above configuration? Note that I am using a rather old ess
version but the I haven't experienced issues with the newer one.
Best regards
Jeremie
> Hi Jeremie,
>
> I just tested with
>
> Org mode version 9.5.3 (release_9.5.3-504-gcdbb1c @
> /home/heinrich/.emacs.d/straight/repos/org/lisp/)
>
> using
>
> GNU Emacs 27.1 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.30, cairo version 1.16.0) of 2021-
> 11-27, modified by Debian
>
> I am on Debian Testing and that is the default emacs version.
>
> Using the unmodified org (git hash from above) I get the following messages when executing a src
> block with R:
>
> executing R code block...
> Loading ‘ess-bugs-l’: unescaped character literals `?(', `?)' detected, `?\(', `?\)' expected!
> Type C-h m for help on ESS version 15.09
> ess-tracebug mode enabled
> Quit
> Package cl is deprecated
>
> Note that the "Quit" is me pressing Ctrl-g after a few seconds.
>
> Removing the commit in question makes the block return instantaneously:
>
> executing R code block...
> Loading ‘ess-bugs-l’: unescaped character literals `?(', `?)' detected, `?\(', `?\)' expected!
> Type C-h m for help on ESS version 15.09
> ess-tracebug mode enabled
> Code block evaluation complete.
> Package cl is deprecated
>
> I anticipated that this would not be obvious, since this feature is used too much to go unnoticed for
> two years - but I am clueless as to how I should continue with debugging...
>
> Thanks for your help!
> Christian
>
> On Sun, 2022-05-15 at 16:16 +0200, Jeremie Juste wrote:
>>
>> Hello Christian,
>>
>> Thanks for reporting but I cannot reproduce the bug with the org and
>> emacs version below.
>>
>> Org mode version 9.5.3 (release_9.5.3-467-g2bd34e @
>> /home/djj/src/org-mode/lisp/)
>> GNU Emacs 27.2 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.24) of
>> 2022-01-16
>>
>> Can you please let me know which version of org-mode you are actually
>> using?
>>
>> Ihor, many thanks for checking.
>>
>> Best regards,
>> Jeremie
>>
>> On Sunday, 15 May 2022 at 16:08, Ihor Radchenko wrote:
>> > Christian Heinrich <com-orgmode-mailinglist@gladbachcity.de> writes:
>> >
>> > > I got back to an org file after upgrading to the latest release of org-mode and tried
>> > > executing the
>> > > contained R source blocks. Unfortunately, emacs got stuck in the execution and was blocked; I
>> > > had to
>> > > exit using C-g.
>> > >
>> > > Here's a minimal example src block that causes emacs to get stuck:
>> > >
>> > > #+begin_src R :results output :session *R* :exports both
>> > > a <- 10
>> > > a
>> > > #+end_src
>> > >
>> > > R itself does start and the code is also executed correctly. However, the output from that
>> > > session
>> > > is apparently not returned to emacs or the buffer.
>> >
>> > I tried you example using Emacs >=26 and it works just fine.
>> >
>> > Best,
>> > Ihor
^ permalink raw reply [flat|nested] 10+ messages in thread
* Re: Bug: ob-R.el breaks when :session is specified
2022-05-15 22:21 ` Jeremie Juste
@ 2022-05-16 5:23 ` Christian Heinrich
2022-05-16 5:24 ` Christian Heinrich
1 sibling, 0 replies; 10+ messages in thread
From: Christian Heinrich @ 2022-05-16 5:23 UTC (permalink / raw)
To: emacs-orgmode
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Hi Jeremie,
thank you for providing this example!
The ess that was found in the load path was years old and once updated, all issues were resolved. In
fact, my so-called minimum init still used (require 'package) and I didn't even think about ESS
causing this trouble.
It's now a bit clearer how to build a real minimum init - thank you!
This is hence resolved.
Best regards
Christian
On Mon, 2022-05-16 at 00:21 +0200, Jeremie Juste wrote:
>
> Hello Christian
>
> On Sunday, 15 May 2022 at 20:06, Christian Heinrich wrote:
> > I just tested with
> >
> > Org mode version 9.5.3 (release_9.5.3-504-gcdbb1c @
> > /home/heinrich/.emacs.d/straight/repos/org/lisp/)
> >
> > using
> >
> > GNU Emacs 27.1 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.30, cairo version 1.16.0) of
> > 2021-
> > 11-27, modified by Debian
>
>
> Many thanks for reporting back. I updated to gcdbb1c and it is still working fine.
>
> My minimum working example is the following. From the org-mode root directory,
>
> $ emacs -Q -L ./lisp -l org -l ~/ess-barebone.el
>
> where ~/ess-barebone.el is the following:
>
> #+begin_src elisp
> (add-to-list 'load-path "/home/djj/.emacs.d/elpa/ess-20220125.2207/")
> (require 'ess-r-mode)
>
> (org-babel-do-load-languages
> 'org-babel-load-languages
> '((R . t)))
>
> (setq org-confirm-babel-evaluate nil)
> #+end_src
>
> Note that I'm still using a rather old ess version. Could you please try
> with the above configuration? Note that I am using a rather old ess
> version but the I haven't experienced issues with the newer one.
>
> Best regards
> Jeremie
>
>
> > Hi Jeremie,
> >
> > I just tested with
> >
> > Org mode version 9.5.3 (release_9.5.3-504-gcdbb1c @
> > /home/heinrich/.emacs.d/straight/repos/org/lisp/)
> >
> > using
> >
> > GNU Emacs 27.1 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.30, cairo version 1.16.0) of
> > 2021-
> > 11-27, modified by Debian
> >
> > I am on Debian Testing and that is the default emacs version.
> >
> > Using the unmodified org (git hash from above) I get the following messages when executing a src
> > block with R:
> >
> > executing R code block...
> > Loading ‘ess-bugs-l’: unescaped character literals `?(', `?)' detected, `?\(', `?\)'
> > expected!
> > Type C-h m for help on ESS version 15.09
> > ess-tracebug mode enabled
> > Quit
> > Package cl is deprecated
> >
> > Note that the "Quit" is me pressing Ctrl-g after a few seconds.
> >
> > Removing the commit in question makes the block return instantaneously:
> >
> > executing R code block...
> > Loading ‘ess-bugs-l’: unescaped character literals `?(', `?)' detected, `?\(', `?\)'
> > expected!
> > Type C-h m for help on ESS version 15.09
> > ess-tracebug mode enabled
> > Code block evaluation complete.
> > Package cl is deprecated
> >
> > I anticipated that this would not be obvious, since this feature is used too much to go
> > unnoticed for
> > two years - but I am clueless as to how I should continue with debugging...
> >
> > Thanks for your help!
> > Christian
> >
> > On Sun, 2022-05-15 at 16:16 +0200, Jeremie Juste wrote:
> > >
> > > Hello Christian,
> > >
> > > Thanks for reporting but I cannot reproduce the bug with the org and
> > > emacs version below.
> > >
> > > Org mode version 9.5.3 (release_9.5.3-467-g2bd34e @
> > > /home/djj/src/org-mode/lisp/)
> > > GNU Emacs 27.2 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.24) of
> > > 2022-01-16
> > >
> > > Can you please let me know which version of org-mode you are actually
> > > using?
> > >
> > > Ihor, many thanks for checking.
> > >
> > > Best regards,
> > > Jeremie
> > >
> > > On Sunday, 15 May 2022 at 16:08, Ihor Radchenko wrote:
> > > > Christian Heinrich <com-orgmode-mailinglist@gladbachcity.de> writes:
> > > >
> > > > > I got back to an org file after upgrading to the latest release of org-mode and tried
> > > > > executing the
> > > > > contained R source blocks. Unfortunately, emacs got stuck in the execution and was
> > > > > blocked; I
> > > > > had to
> > > > > exit using C-g.
> > > > >
> > > > > Here's a minimal example src block that causes emacs to get stuck:
> > > > >
> > > > > #+begin_src R :results output :session *R* :exports both
> > > > > a <- 10
> > > > > a
> > > > > #+end_src
> > > > >
> > > > > R itself does start and the code is also executed correctly. However, the output from that
> > > > > session
> > > > > is apparently not returned to emacs or the buffer.
> > > >
> > > > I tried you example using Emacs >=26 and it works just fine.
> > > >
> > > > Best,
> > > > Ihor
>
[-- Attachment #2: This is a digitally signed message part --]
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^ permalink raw reply [flat|nested] 10+ messages in thread
* Re: Bug: ob-R.el breaks when :session is specified
2022-05-15 22:21 ` Jeremie Juste
2022-05-16 5:23 ` Christian Heinrich
@ 2022-05-16 5:24 ` Christian Heinrich
1 sibling, 0 replies; 10+ messages in thread
From: Christian Heinrich @ 2022-05-16 5:24 UTC (permalink / raw)
To: emacs-orgmode
[-- Attachment #1: Type: text/plain, Size: 4820 bytes --]
Hi Jeremie,
thank you for providing this example!
The ess that was found in the load path was years old and once updated, all issues were resolved. In
fact, my so-called minimum init still used (require 'package) and I didn't even think about ESS
causing this trouble.
It's now a bit clearer how to build a real minimum init - thank you!
This is hence resolved.
Best regards
Christian
On Mon, 2022-05-16 at 00:21 +0200, Jeremie Juste wrote:
>
> Hello Christian
>
> On Sunday, 15 May 2022 at 20:06, Christian Heinrich wrote:
> > I just tested with
> >
> > Org mode version 9.5.3 (release_9.5.3-504-gcdbb1c @
> > /home/heinrich/.emacs.d/straight/repos/org/lisp/)
> >
> > using
> >
> > GNU Emacs 27.1 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.30, cairo version 1.16.0) of
> > 2021-
> > 11-27, modified by Debian
>
>
> Many thanks for reporting back. I updated to gcdbb1c and it is still working fine.
>
> My minimum working example is the following. From the org-mode root directory,
>
> $ emacs -Q -L ./lisp -l org -l ~/ess-barebone.el
>
> where ~/ess-barebone.el is the following:
>
> #+begin_src elisp
> (add-to-list 'load-path "/home/djj/.emacs.d/elpa/ess-20220125.2207/")
> (require 'ess-r-mode)
>
> (org-babel-do-load-languages
> 'org-babel-load-languages
> '((R . t)))
>
> (setq org-confirm-babel-evaluate nil)
> #+end_src
>
> Note that I'm still using a rather old ess version. Could you please try
> with the above configuration? Note that I am using a rather old ess
> version but the I haven't experienced issues with the newer one.
>
> Best regards
> Jeremie
>
>
> > Hi Jeremie,
> >
> > I just tested with
> >
> > Org mode version 9.5.3 (release_9.5.3-504-gcdbb1c @
> > /home/heinrich/.emacs.d/straight/repos/org/lisp/)
> >
> > using
> >
> > GNU Emacs 27.1 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.30, cairo version 1.16.0) of
> > 2021-
> > 11-27, modified by Debian
> >
> > I am on Debian Testing and that is the default emacs version.
> >
> > Using the unmodified org (git hash from above) I get the following messages when executing a src
> > block with R:
> >
> > executing R code block...
> > Loading ‘ess-bugs-l’: unescaped character literals `?(', `?)' detected, `?\(', `?\)'
> > expected!
> > Type C-h m for help on ESS version 15.09
> > ess-tracebug mode enabled
> > Quit
> > Package cl is deprecated
> >
> > Note that the "Quit" is me pressing Ctrl-g after a few seconds.
> >
> > Removing the commit in question makes the block return instantaneously:
> >
> > executing R code block...
> > Loading ‘ess-bugs-l’: unescaped character literals `?(', `?)' detected, `?\(', `?\)'
> > expected!
> > Type C-h m for help on ESS version 15.09
> > ess-tracebug mode enabled
> > Code block evaluation complete.
> > Package cl is deprecated
> >
> > I anticipated that this would not be obvious, since this feature is used too much to go
> > unnoticed for
> > two years - but I am clueless as to how I should continue with debugging...
> >
> > Thanks for your help!
> > Christian
> >
> > On Sun, 2022-05-15 at 16:16 +0200, Jeremie Juste wrote:
> > >
> > > Hello Christian,
> > >
> > > Thanks for reporting but I cannot reproduce the bug with the org and
> > > emacs version below.
> > >
> > > Org mode version 9.5.3 (release_9.5.3-467-g2bd34e @
> > > /home/djj/src/org-mode/lisp/)
> > > GNU Emacs 27.2 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.24) of
> > > 2022-01-16
> > >
> > > Can you please let me know which version of org-mode you are actually
> > > using?
> > >
> > > Ihor, many thanks for checking.
> > >
> > > Best regards,
> > > Jeremie
> > >
> > > On Sunday, 15 May 2022 at 16:08, Ihor Radchenko wrote:
> > > > Christian Heinrich <com-orgmode-mailinglist@gladbachcity.de> writes:
> > > >
> > > > > I got back to an org file after upgrading to the latest release of org-mode and tried
> > > > > executing the
> > > > > contained R source blocks. Unfortunately, emacs got stuck in the execution and was
> > > > > blocked; I
> > > > > had to
> > > > > exit using C-g.
> > > > >
> > > > > Here's a minimal example src block that causes emacs to get stuck:
> > > > >
> > > > > #+begin_src R :results output :session *R* :exports both
> > > > > a <- 10
> > > > > a
> > > > > #+end_src
> > > > >
> > > > > R itself does start and the code is also executed correctly. However, the output from that
> > > > > session
> > > > > is apparently not returned to emacs or the buffer.
> > > >
> > > > I tried you example using Emacs >=26 and it works just fine.
> > > >
> > > > Best,
> > > > Ihor
>
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^ permalink raw reply [flat|nested] 10+ messages in thread
* Re: Bug: ob-R.el breaks when :session is specified
2022-05-15 19:58 ` Berry, Charles
@ 2022-05-16 5:26 ` Christian Heinrich
0 siblings, 0 replies; 10+ messages in thread
From: Christian Heinrich @ 2022-05-16 5:26 UTC (permalink / raw)
To: emacs-orgmode
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Hi Charles,
ob-R.el requires ess and the (require 'package) makes sure the ~/.emacs.d/elpa/ directory was added
to the load path. But you were somewhat right already: the loaded ESS was years old and caused the
issue.
Thanks for your help!
Christian
On Sun, 2022-05-15 at 19:58 +0000, Berry, Charles wrote:
>
> Um...
>
> > On May 15, 2022, at 2:46 AM, Christian Heinrich <com-orgmode-mailinglist@gladbachcity.de> wrote:
> >
> > I run
> >
> > emacs -q --load /tmp/init.el --file=/tmp/test.org
> >
> > with my /tmp/init.el being only
> >
> > > (require 'package)
> > > (package-initialize)
> > > (add-to-list 'load-path "~/.emacs.d/straight/repos/org/lisp/")
> > > (require 'org)
> > >
> > > ;(require 'ess-site)
>
> The line above is commented out. So how do you load ess-site?
>
>
> > > (org-babel-do-load-languages
> > > 'org-babel-load-languages
> > > '((R . t)))
> >
> > I hope this constitutes a minimal example for a config - please correct me if I'm wrong.
>
>
> Just spitballing here:
>
> Have you tried instrumenting `org-babel-R-evaluate-session'?
>
> Maybe watching changes made to the session buffer on first evaluation and comparing to subsequent
> evals helps.
>
> HTH,
> Chuck
>
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^ permalink raw reply [flat|nested] 10+ messages in thread
end of thread, other threads:[~2022-05-16 5:30 UTC | newest]
Thread overview: 10+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2022-05-15 6:00 Bug: ob-R.el breaks when :session is specified Christian Heinrich
2022-05-15 8:08 ` Ihor Radchenko
2022-05-15 9:46 ` Christian Heinrich
2022-05-15 19:58 ` Berry, Charles
2022-05-16 5:26 ` Christian Heinrich
2022-05-15 14:16 ` Jeremie Juste
2022-05-15 18:06 ` Christian Heinrich
2022-05-15 22:21 ` Jeremie Juste
2022-05-16 5:23 ` Christian Heinrich
2022-05-16 5:24 ` Christian Heinrich
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